DO NOT test this on the dummies in Shrine. There is an issue on them where they're too close to the wall, causing the pet to sometimes clip through the wall and lose line-of-sight (which is now needed for the changes to Basic Attacks made during implementing Blink Strikes). Test it on a dummy like the one in Darnassus, with a large area of space behind it.
I've personally not seen this happen, outside of the specific instance of the Shrine dummies (which is an issue which should not occur on any of the raid bosses, as far as I'm aware -- and certainly not on all of them).
There did also used to be a bug back in... Cataclysm where autocast settings (though this was setting autocast off) wouldn't stick intermittently unless the ability was on the pet bar. Can anyone confirm whether they've seen this autocast issue with any ability that is on their pet bar?